anndata - Annotated data#
anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.
Discuss development on GitHub.
Read the documentation.
Ask questions on the scverse Discourse.
pip install anndataor
conda install anndata -c conda-forge.
See Scanpy’s documentation for usage related to single cell data. anndata was initially built for Scanpy.
anndata is part of the scverse project (website, governance) and is fiscally sponsored by NumFOCUS. Please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
If you use
anndata in your work, please cite the
anndata pre-print as follows:
anndata: Annotated data
Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, F. Alexander Wolf
bioRxiv 2021 Dec 19. doi: 10.1101/2021.12.16.473007.
You can cite the scverse publication as follows:
The scverse project provides a computational ecosystem for single-cell omics data analysis
Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis
Nat Biotechnol. 2023 Apr 10. doi: 10.1038/s41587-023-01733-8.
0.10.4 the future#
Added compatibility layer for packages relying on
anndata._core.sparse_dataset.SparseDataset. Note that this API is deprecated and new code should use
sparse_dataset()instead. #1185 @ivirshup
Once you have
CuPyarrays in your anndata, use it with:
Out of core
Improved errors and warnings
See Release notes for more.
Muon paper published 2022-02-02#
Muon has been published in Genome Biology [^cite_bredikhin22].
Muon is a framework for multimodal data built on top of
COVID-19 datasets distributed as
In a joint initiative, the Wellcome Sanger Institute, the Human Cell Atlas, and the CZI distribute datasets related to COVID-19 via anndata’s
h5ad files: covid19cellatlas.org.